SMTL ID : 4bgk.1

Three dimensional structure of human gamma-butyrobetaine hydroxylase in complex with (3-(Trimethylammonio)propyl)phosphinate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

homo-dimer

Ligands

2 x OGA: N-OXALYLGLYCINE(Non-covalent)

OGA.1: 12 residues within 4Å: Chain A: V.183, A.193, L.199, H.202, D.204, L.217, H.347, R.349, R.360, L.362 Ligands: RTK.2, ZN.3 4 PLIP interactions: 4 interactions with chain A Water bridges: A:S.229 Salt bridges: A:H.202, A:R.349, A:R.360 OGA.6: 12 residues within 4Å: Chain B: V.183, A.193, L.199, H.202, D.204, L.217, H.347, R.349, R.360, L.362 Ligands: RTK.7, ZN.8 4 PLIP interactions: 4 interactions with chain B Water bridges: B:S.229 Salt bridges: B:H.202, B:R.349, B:R.360

2 x RTK: trimethyl(3-oxidanylphosphonoylpropyl)azanium(Non-covalent)

RTK.2: 12 residues within 4Å: Chain A: Y.177, W.181, N.191, A.193, Y.194, D.204, Y.205, P.206, N.292, T.295, Y.366 Ligands: OGA.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.177 Hydrogen bonds: A:N.191, A:Y.205, A:N.292 Water bridges: A:D.261, A:T.295 Salt bridges: A:D.204 pi-Cation interactions: A:Y.177, A:W.181 RTK.7: 12 residues within 4Å: Chain B: Y.177, W.181, N.191, A.193, Y.194, D.204, Y.205, P.206, N.292, T.295, Y.366 Ligands: OGA.6 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.177 Hydrogen bonds: B:N.191, B:Y.205, B:N.292 Water bridges: B:D.261, B:T.295, B:T.295 Salt bridges: B:D.204 pi-Cation interactions: B:Y.177, B:W.181

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.202, D.204, H.347 Ligands: OGA.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.202, A:D.204, A:H.347 ZN.4: 4 residues within 4Å: Chain A: C.38, C.40, C.43, H.82 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.38, A:C.40, A:C.43, A:H.82 ZN.8: 4 residues within 4Å: Chain B: H.202, D.204, H.347 Ligands: OGA.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.202, B:D.204, B:H.347 ZN.9: 4 residues within 4Å: Chain B: C.38, C.40, C.43, H.82 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.38, B:C.40, B:C.43, B:H.82

2 x 16D: HEXANE-1,6-DIAMINE(Non-covalent)

16D.5: 2 residues within 4Å: Chain A: Y.75, Y.83 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.83 Hydrogen bonds: A:Y.75 16D.10: 2 residues within 4Å: Chain B: Y.75, Y.83 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.83 Hydrogen bonds: B:Y.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tars, K. et al., Targeting Carnitine Biosynthesis: Discovery of New Inhibitors Against Gamma-Butyrobetaine Hydroxylase. J.Med.Chem. (2014)

Release Date

2014-03-12

Peptides

GAMMA-BUTYROBETAINE DIOXYGENASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

GAMMA-BUTYROBETAINE DIOXYGENASE

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